| Types of MSA alignment | MSA algorithms |
| Pairwise alignment | Needleman-Wunsch, k-mer, k-tuple, and Smith-Waterman algorithms. | Progressive alignment | Clustal Omega, ClustalW, MAFFT, Kalign, Probalign, MUSCLE, Dialign, ProbCons, and MSAProbs. | Iterative progressive alignment | PRRP, MUSCLE, DIALIGN, SAGA, and T-COFFEE. | Homology search tools | BLAST, PSI-BLAST, and FASTA. | Structure incorporating alignment | 3D-COFFEE, EXPRESSO, and MICAlign. | Motif alignment | PHI-Blast, GLAM2. | Short-read alignment | Bowtie, Maq, and SOAP. |
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